Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate SMc03814 SMc03814 ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Smeli:SMc03814 Length = 335 Score = 157 bits (396), Expect = 5e-43 Identities = 102/313 (32%), Positives = 158/313 (50%), Gaps = 11/313 (3%) Query: 52 WFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAI 111 W +A++V+ L+V I+ +F L ++ +A + + ALG VL SGGID+S +I Sbjct: 33 WIALAILVIG-LVVSVISAKFATSGNLLNIFQNACFIGIMALGMTPVLISGGIDISVGSI 91 Query: 112 AALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYL 171 L M G+T + D P A+ ++ GV GMVNG+++ +K P IVT+ T + Sbjct: 92 --LGMCGVTLGIVLN-SDMPLAVGILATLAMGVACGMVNGIIISYVKLPPFIVTLATLSI 148 Query: 172 YRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLL 231 R L L F FGR G LP V ALVA ++ +LL Sbjct: 149 GRSLALVLTNNEVFYE-------FGRATNGIIALGGGYSFGLPNVVYALVAGVIILHFLL 201 Query: 232 NRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDL 291 T GR ++A+GG+ A A G + I + + + G++ I + V Sbjct: 202 TMTRWGRYLFAIGGNEAAARLAGIPVDLIKVSAYAFNGLMVAITAVFLVGWLGAVTNAIG 261 Query: 292 VGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFI 351 G EL VIA+ ++GGA +TGG GT +G +G +LV +I++ L++ GV WQ + +G+FI Sbjct: 262 TGYELQVIASTVIGGASLTGGFGTALGAAIGAILVEVIRNALLIAGVNPFWQGMFVGSFI 321 Query: 352 LLAGTLFALQRKR 364 L A L ++ R Sbjct: 322 LAAVLLERIRSLR 334 Lambda K H 0.328 0.141 0.426 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 295 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 364 Length of database: 335 Length adjustment: 29 Effective length of query: 335 Effective length of database: 306 Effective search space: 102510 Effective search space used: 102510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory